Whole-genome sequencing for rapid, reliable and routine investigation of Mycobacterium tuberculosis transmission in local communities.

Contact investigations following the diagnosis of active tuberculosis (TB) are paramount for the control of the disease. Epidemiological data are very powerful for contact tracing but might be delayed and/or difficult to integrate, especially in the setting of multiple contact-tracing investigations. The aim of this study was to address the added-value of whole-genome sequencing (WGS) to routine local TB surveillance systems. From November 2016 to July 2017, the local TB surveillance system identified three clusters that could constitute a unique larger outbreak. Epidemiological and clinical information were integrated with WGS genotyping data of Mycobacterium tuberculosis strains obtained using a simple DNA extraction method coupled with sequencing using an Illumina MiSeq platform and an in-house bioinformatics pipeline for single nucleotide polymorphism (SNP) analysis. Epidemiological investigations identified three putative TB clusters potentially interrelated including eight patients with active TB. Seven M. tuberculosis isolates were available and analysed by WGS. Using a 5-SNP threshold to define recent transmission, WGS-based genotyping supported the occurrence of the three clusters as well as a link between clusters 1 and 2 (SNP ≤1), constituting a larger outbreak. This outbreak was clearly delineated by refuting a potential link with the third cluster (SNP >500). Genotyping data did not support the belonging of patient 7 to any studied cluster. This study illustrates the usefulness of WGS genotyping for routine TB surveillance systems in local communities to rapidly confirm or disprove epidemiological hypotheses and delineate TB clusters, especially in the context of multiple contact-tracing investigations.

Odontoblastic differentiation of dental pulp stem cells from healthy and carious teeth on an original PCL-based 3D scaffold.

AIMS: To isolate and characterize dental pulp stem cells (DPSCs) obtained from carious and healthy mature teeth extracted when conservative treatment was not possible or for orthodontic reasons; to evaluate the ability of DPSCs to colonize, proliferate and differentiate into functional odontoblast-like cells when cultured onto a polycaprolactone cone made by jet-spraying and prototyped into a design similar to a gutta-percha cone. METHODOLOGY: DPSCs were obtained from nine carious and 12 healthy mature teeth. Then cells were characterized by flow cytometry and submitted to multidifferentiation to confirm their multipotency. These DPSCs were then cultured on a polycaprolactone cone in an odontoblastic differentiation medium. Cell proliferation, colonization of the biomaterial and functional differentiation of cells were histologically assessed. For the characterization, a t-Student test was used to compare the two groups. RESULTS: In all cell cultures, characterization highlighted a mesenchymal stem cell phenotype (CD105+, CD90+, CD73+, CD11b-, CD34-, CD45-, HLA-DR-). No significant differences were found between cultures obtained from carious and healthy mature teeth. DPSCs from both origins were able to differentiate into osteocytes, adipocytes and chondrocytes. Cell colonization was observed both on the surface and in the thickness of polycaprolactone cones as well as a mineralized pericellular matrix deposit composed of type I collagen, alkaline phosphatase, osteocalcin and dentin sialophosphoprotein. CONCLUSIONS: DPSCs were isolated from both carious and healthy mature teeth. They were able to colonize and proliferate within a polycaprolactone cone and could be differentiated into functional odontoblast-like cells.

Ochroconis gallopava bronchitis mimicking haemoptysis in a patient with bronchiectasis.

Ochroconis gallopava is an anamorphic mould characterized by slow growth rate and production of a maroon pigment, which has been isolated worldwide from soil, thermal springs, decaying vegetation, and chicken litter. It has been reported to cause localized, mostly pulmonary, and systemic infection in severely immunocompromised patients. We describe the case of a 76-year-old woman known for ulcerative colitis-related bronchiectasis treated with low dose oral steroids, who developed a fungal bronchitis with dark, bloody-like, sputum which was initially misinterpreted as haemoptysis. A filamentary mould grew on sputum culture, and was identified by DNA analysis as Ochroconis gallopava. We observed a significant clinical improvement after 6 weeks of itraconazole therapy.

[The asthma-COPD overlap syndrome]. / Le syndrome de chevauchement asthme-BPCO.

Asthma and COPD are often considered mutually exclusive diseases, mainly because of the inclusion of only typical cases of asthma or COPD in therapeutic clinical trials. However, clinicians are unable to distinguish between both conditions in a substantial number of patients, a situation that may be called the "asthma-COPD overlap syndrome". It is important to recognize this entity, as patients suffering from an asthma-COPD overlap syndrome are more symptomatic, have a poorer quality of life and suffer more exacerbations than patients with asthma or COPD alone. In the absence of studies specifically designed to assess the treatment modalities for these patients, it appears wise to prescribe inhaled corticosteroids early in the course of the disease, considering their established efficacy in asthma.

[Chronic obstructive pulmonary disease and its links with cardiovascular risk factors]. / La bronchopneumopathie chronique obstructive et son lien avec les facteurs de risque cardiovasculaires.

Patients with chronic obstructive pulmonary disease (COPD) often also present with one or more cardiovascular risk factors, resulting not only in an increased mortality rate but also in a major impact on the health care system. Aside from common predisposing and environmental factors, the hypothesis of a chronic systemic inflammation linking COPD and cardiovascular co-morbidities is supported by an increasing body of evidence in recent literature. This could in turn pave the way for new developments, both diagnostic and therapeutic, in the future. In this context, the studies CoLaus and PneumoLaus aim to further investigate characteristics of the Lausanne general population, in particular those relating to cardiovascular and respiratory disease.

[Lung abscess: changes in treatment?]. / Abcès pulmonaires: évolution dans la prise en charge?

Lung abscess occurs in very pleomorphic according to germs initially involved. The mechanism commonly found is an aspiration of the oropharyngeal flora in patients with disorders of consciousness or swallowing. The infection is polymicrobial, with presence of anaerobic germs in 2/3 of the cases. The support consists of a prolonged antibiotic treatment, as well as anaerobic until resolution or stability of the radiological image. In case of prolonged toxic state, drainage of the abscess is to be discussed especially if there is no airways drainage. Surgical sanctions is rarely needed regardless of the size of the abscess, unless underlying carcinoma is present.

From surface to intracellular non-invasive nanoscale study of living cells impairments.

Among the enduring challenges in nanoscience, subsurface characterization of living cells holds major stakes. Developments in nanometrology for soft matter thriving on the sensitivity and high resolution benefits of atomic force microscopy have enabled detection of subsurface structures at the nanoscale. However, measurements in liquid environments remain complex, in particular in the subsurface domain. Here we introduce liquid-mode synthesizing atomic force microscopy (l-MSAFM) to study both the inner structures and the chemically induced intracellular impairments of living cells. Specifically, we visualize the intracellular stress effects of glyphosate on living keratinocytes skin cells. This new approach, l-MSAFM, for nanoscale imaging of living cell in their physiological environment or in presence of a chemical stress agent could resolve the loss of inner structures induced by glyphosate, the main component of a well-known pesticide (RoundUp™). This firsthand ability to monitor the cell's inner response to external stimuli non-destructively and in liquid, has the potential to unveil critical nanoscale mechanisms of life science.

[Lung volume reduction (LVR) in severe emphysema: a multidisciplinary approach]. / Réduction de volume pulmonaire dans l'emphysème sévère: importance d'une prise en charge multidisciplinaire.

Most cases of emphysema are managed conservatively. However, in severe symptomatic emphysema associated with hyperinflation, lung volume reduction (LVR) may be proposed to improve dyspnea, exercice capacity, pulmonary functions, walk distance and to decrease long-term mortality. LVR may be achieved either surgically (LVRS) or endoscopically (EVLR by valves or coils) according to specific clinical criteria. Currently, the optimal approach is discussed in a multidisciplinary setting. The latter permits a personalized evaluation the patient's clinical status and allows the best possible therapeutic intervention to be proposed to the patient.

Thymic stromal lymphopoietin plays divergent roles in murine models of atopic and nonatopic airway inflammation.

BACKGROUND: Thymic stromal lymphopoietin (TSLP) is a cytokine primarily produced by epithelial cells, which has been shown to be a potent inducer of T-helper 2 (Th2)-type responses. However, TSLP has pleiotropic effects upon immune cells, and although extensively studied in the context of atopic asthma, its relevance as a therapeutic target and its role in the pathogenesis of nonatopic asthma remains unknown. We sought to investigate the role of TSLP in atopic, nonatopic and viral-induced exacerbations of pulmonary inflammation. METHODS: Using stringently defined murine models of atopic, nonatopic and virally exacerbated forms of pulmonary inflammation, we compared inflammatory responses of C57BL/6 wild-type (WT) and TSLP receptor-deficient (TSLPR KO) mice. RESULTS: Thymic stromal lymphopoietin receptor (TSLPR) signaling was crucial for the development of atopic asthma. Specifically, TSLPR signaling to lung recruited CD4+ T cells enhanced eosinophilia, goblet cell hyperplasia, and overall inflammation within the airways. In contrast, the absence of TSLPR signaling was associated with strikingly exaggerated pulmonary neutrophilic inflammation in a nonatopic model of airway inflammation. The inflammation was associated with excessive levels of interleukin (IL)-17A in the lungs, indicating that TSLP negatively regulates IL-17A. In addition, in a model of influenza-induced exacerbation of atopic airway inflammation, the absence of TSLPR signaling also led to exaggerated neutrophilic inflammation. CONCLUSION: Thymic stromal lymphopoietin plays divergent roles in the pathogenesis of atopic and nonatopic asthma phenotypes by either enhancing Th2 responses or curtailing T-helper 17 responses. These findings raise important caveats for the design of therapeutic interventions targeting TSLP in asthma.

Incidence and outcomes of respiratory viral infections in lung transplant recipients: a prospective study.

BACKGROUND: The incidence and outcomes of respiratory viral infections in lung transplant recipients (LTR) are not well defined. The objective of this prospective study conducted from June 2008 to March 2011 was to characterise the incidence and outcomes of viral respiratory infections in LTR. METHODS: Patients were seen in three contexts: study-specific screenings covering all seasons; routine post-transplantation follow-up; and emergency visits. Nasopharyngeal specimens were collected systematically and bronchoalveolar lavage (BAL) was performed when clinically indicated. All specimens underwent testing with a wide panel of molecular assays targeting respiratory viruses. RESULTS: One hundred and twelve LTR had 903 encounters: 570 (63%) were screening visits, 124 (14%) were routine post-transplantation follow-up and 209 (23%) were emergency visits. Respiratory viruses were identified in 174 encounters, 34 of these via BAL. The incidence of infection was 0.83 per patient-year (95% CI 0.45 to 1.52). The viral infection rates upon screening, routine and emergency visits were 14%, 15% and 34%, respectively (p<0.001). Picornavirus was identified most frequently in nasopharyngeal (85/140; 60.7%) and BAL specimens (20/34; 59%). Asymptomatic viral carriage, mainly of picornaviruses, was found at 10% of screening visits. Infections were associated with transient lung function loss and high calcineurin inhibitor blood levels. The hospitalisation rate was 50% (95% CI 30% to 70.9%) for influenza and parainfluenza and 16.9% (95% CI 11.2% to 23.9%) for other viruses. Acute rejection was not associated with viral infection (OR 0.4, 95% CI 0.1 to 1.3). CONCLUSIONS: There is a high incidence of viral infection in LTR; asymptomatic carriage is rare. Viral infections contribute significantly to this population's respiratory symptomatology. No temporal association was observed between infection and acute rejection.

[Lungs et diving]. / Poumons et plongée subaquatique.

Whilst underwater, the body is submitted to significant variations of the surrounding pressure according to the depth. These conditions modify the hemodynamic and the ventilatory mechanics considerably. Some repercussions, like pulmonary barotrauma, are related to simple physical phenomena. Others, like decompression sickness, are due to more com- plex processes. Breath-hold diving disrupts haematosis and can be complicated by alveolar haemorrhage and loss of consciousness. Acute pulmonary oedema during scuba-diving, breath-hold diving and swimming has been reported more recently. In case of pulmonary disorders scuba-diving is contraindicated most of the time. It is therefore highly recommended to seek medical advice to prevent problems.

[Idiopathic pulmonary fibrosis: recent diagnostic and therapeutic advances]. / Fibrose pulmonaire idiopathique: nouveautés diagnostiques et thérapeutiques.

Idiopathic pulmonary fibrosis (IPF) is the most frequent of the idiopathic interstitial pneumonias. It is a progressive disorderwith a poor prognosis. Its diagnosis requires the careful exclusion of potential causes, and a pattern of usual interstitial pneumonia at high-resolution computed tomography or video-assisted surgical lung biopsy. Several recent randomized trials have profoundly modified the therapeutic management of IPF. The combination of prednisone and azathioprine, often prescribed until recently, has been shown to be harmful and is no longer indicated. N-acetylcystein, also used in the past decade, failed to show an efficacy. However, two new antifibrotic drugs, pirfenidone and nintedanib, have for the first time proven effective in slowing disease progression.

[Granulomatous lymphocytic interstitial lung disease in common variable immunodeficiency]. / Pneumopathie interstitielle granulomato-lymphocytaire dans l'immunodéficience commune variable.

Common variable immunodeficiency (CVID) is the most frequent primary immune deficiency. Recurrent infections are classical consequences of CVID, but their impact has been largely reduced by immunoglobulin replacement. CVID is also associated with various inflammatory and autoimmune manifestations resulting from abnormal cellular immunity. The lungs are especially affected by a recently described entity called granulomatous lymphocytic interstitial lung disease (GLILD). GLILD currently constitutes an important cause of morbidity and mortality in these patients. It is distinct from bronchiectasis secondary to recurrent infections, and presents similarities but also striking differences with sarcoidosis.

[Pulmonary hypertension in left heart disease: how to define it and how to manage it in 2013?]. / Hypertension pulmonaire associée aux maladies du coeur gauche: quelle définition et quelle prise en charge en 2013?

Pulmonary hypertension is a frequent complication of left heart disease arising from a wide range of cardiac disorders and is associated with poor prognosis. Its pathophysiology is complex with both passive mechanisms of elevated filling pressures in left cavities and occasionally reactive mechanisms of arterial vasoconstriction and remodelling to interplay. This stage, called <> pulmonary hypertension, further worsens the heart failure patients' prognosis but is still a matter of debate concerning the criteria to apply for its diagnosis and concerning the best way to manage it. This article gives an overview of the importance and pathophysiology of pulmonary hypertension associated with left heart disease, and discusses the challenges associated with its diagnosis and treatment.